From cb7f2fabddd25a9c51ba557015ecf8e94e244b5f Mon Sep 17 00:00:00 2001
From: Ari Kahn <ari.e.kahn@gmail.com>
Date: Fri, 22 May 2020 10:08:21 -0400
Subject: [PATCH] check for fmriprep res flags

---
 modules/prestats/prestats.mod | 19 +++++++++++++++++--
 modules/task/task.mod         | 18 ++++++++++++++++--
 2 files changed, 33 insertions(+), 4 deletions(-)

diff --git a/modules/prestats/prestats.mod b/modules/prestats/prestats.mod
index b6c1a6fb..5fdf5a81 100755
--- a/modules/prestats/prestats.mod
+++ b/modules/prestats/prestats.mod
@@ -224,10 +224,25 @@ while (( ${#rem} > 0 ))
          
         routine @ getting data from fmriprep directory 
         exec_fsl immv ${intermediate} ${intermediate}_${cur}   
-        imgprt=${img1[sub]%_*_*_*}; conf="_desc-confounds_regressors.tsv"
+
+        # Check if we have a res- tag
+        # Added by recent versions of fmriprep
+        imgname=$(basename ${img1[sub]})
+        conf="_desc-confounds_regressors.tsv"
+        if [[ "$imgname" == *_res-* ]]; then
+           imgprt=${img1[sub]%_*_*_*_*}
+        else
+           imgprt=${img1[sub]%_*_*_*}
+        fi
         exec_sys cp ${imgprt}${conf} $out/prestats/${prefix}_fmriconf.tsv
+
         imgprt2=${img1[sub]%_*_*}; mskpart="_desc-brain_mask.nii.gz"
-        mask1=${imgprt2}${mskpart}; maskpart2=${mask1#*_*_*_*}
+        mask1=${imgprt2}${mskpart};
+        if [[ "$imgname" == *_res-* ]]; then
+           maskpart2=${mask1#*_*_*_*_*}
+        else
+           maskpart2=${mask1#*_*_*_*}
+        fi
         refpart="_boldref.nii.gz"; refvol=${imgprt2}${refpart}
 
         conf2="_desc-confounds_regressors.json"
diff --git a/modules/task/task.mod b/modules/task/task.mod
index fdf3be95..8112416d 100755
--- a/modules/task/task.mod
+++ b/modules/task/task.mod
@@ -205,10 +205,24 @@ if (( ${task_fmriprep[cxt]} == 1 ))
         
          routine @ getting data from frmiprep directory 
                   
-        imgprt=${img1[sub]%_*_*_*}; conf="_desc-confounds_regressors.tsv"
+        # Check if we have a res- tag
+        # Added by recent versions of fmriprep
+        imgname=$(basename ${img1[sub]})
+        conf="_desc-confounds_regressors.tsv"
+        if [[ "$imgname" == *_res-* ]]; then
+          imgprt=${img1[sub]%_*_*_*_*}
+        else
+          imgprt=${img1[sub]%_*_*_*}
+        fi
         exec_sys cp ${imgprt}${conf} ${out}/task/${prefix}_fmriconf.tsv
+
         imgprt2=${img1[sub]%_*_*}; mskpart="_desc-brain_mask.nii.gz"
-        mask1=${imgprt2}${mskpart}; maskpart2=${mask1#*_*_*_*}
+        mask1=${imgprt2}${mskpart};
+        if [[ "$imgname" == *_res-* ]]; then
+           maskpart2=${mask1#*_*_*_*_*}
+        else
+           maskpart2=${mask1#*_*_*_*}
+        fi
         refpart="_boldref.nii.gz"; refvol=${imgprt2}${refpart}
          
        output fmriprepconf  ${out}/task/${prefix}_fmriconf.tsv